grouper: Find groups of correlating samples

In LieberInstitute/brainstorm_package: Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation

Find groups of correlating samples

Description

Create groups of sample from a cor table with correlation >= cutoff

Usage

grouper(corTable, cutoff = 0.59, s1 = "row_sample", s2 = "col_sample")

Arguments

corTable	Table of paiwise correlation between samples
cutoff	corrlation threshold for samples to be grouped together
s1	Name of first column that contains sample names
s2	Name of second column that contains sample names

Value

List of groups found in the cor table

Examples

cor_test <- make_corLong(snps1 = test_snps, BrainTable1 = test_BrTable, ID_col1 = "Sample")
g <- grouper(cor_test)

snpsCalled_filter <- filter_called(snpsCalled_VCF)
snpsRNA <- make_snpsRNA(snpsGeno_VCF, snpsCalled_filter)
pd_simple <- pd_example[,1:4]
corLong_rna <- make_corLong(snpsRNA$snpsCalled, BrainTable1 = pd_simple, ID_col1 = "SAMPLE_ID")
groups_rna <- grouper(corLong_rna)

LieberInstitute/brainstorm_package documentation built on Dec. 14, 2024, 10:29 p.m.